Saturday 11/23/13

10:00a – 11:00p

STORM2

  • Helping Guipeng and Ruobo get set up on STORM2.

Cell staining

  • prepping cells for hybridizaton.
  • last row (4 coverslips) forgot to add last rinse of PBS. Cells dried out. Coverslips tossed.
  • cells into formamide, ready for staining.
  • Samples to test: D8, D10, E3, E11, F3, G4
  • All stained, incubating at 47C, ~7pm

Library / Deep Seq analysis

  • Rebuilt Lib2 fasta with indexed headers (Library2idx.fasta)
  • Re-running bowtie2 on on indexed Lib2 fasta
  • still running at 10pm

Computer

  • Cajal has 12 memory slots and 6x 4Gb currently on board. Could add 4×4 Gb more from Monet upgrade.

Coding

  • Add ROI analysis to STORMfinder
  • To add to Insight, modify .ini file to contain in ‘Image’ field the following lines:
    ROI Valid=1
    ROI_x0=0
    ROI_x1=256
    ROI_y0=0
    ROI_y1=256
  • Sync Monet, Tuck and Cajal Git to use ZhuangLab/storm-analysis git repo as the DaoSTORM location (this will remain updated by hazen).
  • test insight ROI on STORMfinder. Seems to work excellent
  • Investigating new ROI in DaoSTORM
  • successfully integrated ROI specification in STORMfinder / matlab-storm repo.

STORM Analysis

  • Box4 went unresponsive during final stages of analysis of G9 data. Several daoSTORM runs failed, possibly corrupted.
  • Running G1 data on Monet using new ROI finder.
  • synched

STORM imaging

  • set up overnight STORM of E10rna stained cells in V marked region.
  • V clearly visible in 10x image but not in 100x image.
  • hopefully the large cells act as landmarks. Could have tried imaging more beads.

Presentations

  • working on slides for meeting with Ting
  • tentatively scheduled for Dec 3, 2pm.

To address

  • extra F6 data set on STORM2. Is this really F6?! Why would I image F6 on 11/08, I had plenty of F6 before. Check with Bogdan.
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